Starting phenix.real_space_refine on Sat Feb 17 09:28:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yu8_6844/02_2024/5yu8_6844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yu8_6844/02_2024/5yu8_6844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yu8_6844/02_2024/5yu8_6844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yu8_6844/02_2024/5yu8_6844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yu8_6844/02_2024/5yu8_6844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yu8_6844/02_2024/5yu8_6844_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 11496 2.51 5 N 3031 2.21 5 O 3498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18147 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "I" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "J" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.83, per 1000 atoms: 0.54 Number of scatterers: 18147 At special positions: 0 Unit cell: (119.88, 106.92, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 10 15.00 Mg 5 11.99 O 3498 8.00 N 3031 7.00 C 11496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 3.3 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 29 sheets defined 37.3% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.584A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.554A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.690A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.416A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 removed outlier: 3.832A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.803A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.555A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 296' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.533A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 346 removed outlier: 3.679A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.582A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.584A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.554A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.689A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.415A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 removed outlier: 3.831A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.803A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.555A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 296' Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.532A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.679A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 345 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 373 removed outlier: 3.583A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.584A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.553A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.690A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.416A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 216 removed outlier: 3.832A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.803A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 279 through 282 No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 291 through 296 removed outlier: 3.555A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 296' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 310 through 320 removed outlier: 3.533A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 346 removed outlier: 3.679A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 345 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 366 through 373 removed outlier: 3.583A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.583A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.554A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.689A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.416A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 3.832A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.803A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 279 through 282 No H-bonds generated for 'chain 'D' and resid 279 through 282' Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 291 through 296 removed outlier: 3.555A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 291 through 296' Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 310 through 320 removed outlier: 3.533A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 346 removed outlier: 3.679A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE D 345 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 366 through 373 removed outlier: 3.583A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 92 removed outlier: 3.584A pdb=" N GLU E 83 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.554A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.690A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.416A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.832A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.803A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 256 No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 279 through 282 No H-bonds generated for 'chain 'E' and resid 279 through 282' Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 291 through 296 removed outlier: 3.555A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 291 through 296' Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.532A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.679A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE E 341 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE E 345 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 366 through 373 removed outlier: 3.583A pdb=" N ILE E 369 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 69 through 72 No H-bonds generated for 'chain 'H' and resid 69 through 72' Processing helix chain 'H' and resid 111 through 118 removed outlier: 4.106A pdb=" N ILE H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 125 Processing helix chain 'H' and resid 140 through 144 Processing helix chain 'H' and resid 147 through 153 removed outlier: 3.883A pdb=" N LYS H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 19 Processing helix chain 'I' and resid 57 through 59 No H-bonds generated for 'chain 'I' and resid 57 through 59' Processing helix chain 'I' and resid 69 through 72 No H-bonds generated for 'chain 'I' and resid 69 through 72' Processing helix chain 'I' and resid 111 through 118 removed outlier: 4.107A pdb=" N ILE I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'I' and resid 147 through 153 removed outlier: 3.883A pdb=" N LYS I 152 " --> pdb=" O THR I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 19 Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'J' and resid 69 through 72 No H-bonds generated for 'chain 'J' and resid 69 through 72' Processing helix chain 'J' and resid 111 through 118 removed outlier: 4.107A pdb=" N ILE J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 125 Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 147 through 153 removed outlier: 3.883A pdb=" N LYS J 152 " --> pdb=" O THR J 148 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.566A pdb=" N CYS A 10 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.088A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.565A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.088A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.565A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.088A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.566A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.088A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 29 through 32 removed outlier: 7.565A pdb=" N CYS E 10 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.088A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'H' and resid 47 through 49 removed outlier: 3.503A pdb=" N TYR H 89 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS H 133 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE H 103 " --> pdb=" O HIS H 133 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP H 135 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.479A pdb=" N ILE H 55 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 89 through 91 Processing sheet with id= X, first strand: chain 'I' and resid 47 through 49 removed outlier: 3.503A pdb=" N TYR I 89 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS I 133 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE I 103 " --> pdb=" O HIS I 133 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP I 135 " --> pdb=" O PHE I 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 33 through 36 removed outlier: 6.480A pdb=" N ILE I 55 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 89 through 91 Processing sheet with id= AA, first strand: chain 'J' and resid 47 through 49 removed outlier: 3.503A pdb=" N TYR J 89 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS J 133 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE J 103 " --> pdb=" O HIS J 133 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP J 135 " --> pdb=" O PHE J 103 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 33 through 36 removed outlier: 6.480A pdb=" N ILE J 55 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 89 through 91 478 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4541 1.35 - 1.47: 5585 1.47 - 1.59: 8196 1.59 - 1.71: 10 1.71 - 1.83: 183 Bond restraints: 18515 Sorted by residual: bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 ADP D 402 " pdb=" C5 ADP D 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 ADP E 402 " pdb=" C5 ADP E 402 " ideal model delta sigma weight residual 1.490 1.372 0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 18510 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.79: 131 102.79 - 111.06: 6032 111.06 - 119.32: 9121 119.32 - 127.58: 9643 127.58 - 135.85: 146 Bond angle restraints: 25073 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" N GLY D 13 " pdb=" CA GLY D 13 " ideal model delta sigma weight residual 120.10 125.24 -5.14 9.50e-01 1.11e+00 2.93e+01 angle pdb=" C ASN B 12 " pdb=" N GLY B 13 " pdb=" CA GLY B 13 " ideal model delta sigma weight residual 120.10 125.23 -5.13 9.50e-01 1.11e+00 2.91e+01 angle pdb=" C ASN A 12 " pdb=" N GLY A 13 " pdb=" CA GLY A 13 " ideal model delta sigma weight residual 120.10 125.21 -5.11 9.50e-01 1.11e+00 2.89e+01 angle pdb=" C GLY H 4 " pdb=" N VAL H 5 " pdb=" CA VAL H 5 " ideal model delta sigma weight residual 120.49 127.89 -7.40 1.38e+00 5.25e-01 2.88e+01 angle pdb=" C ASN E 12 " pdb=" N GLY E 13 " pdb=" CA GLY E 13 " ideal model delta sigma weight residual 120.10 125.20 -5.10 9.50e-01 1.11e+00 2.88e+01 ... (remaining 25068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 10812 22.76 - 45.52: 321 45.52 - 68.28: 66 68.28 - 91.04: 23 91.04 - 113.80: 5 Dihedral angle restraints: 11227 sinusoidal: 4578 harmonic: 6649 Sorted by residual: dihedral pdb=" C5' ADP D 402 " pdb=" O5' ADP D 402 " pdb=" PA ADP D 402 " pdb=" O2A ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 53.80 -113.80 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" C5' ADP E 402 " pdb=" O5' ADP E 402 " pdb=" PA ADP E 402 " pdb=" O2A ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 53.77 -113.77 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 53.77 -113.77 1 2.00e+01 2.50e-03 3.37e+01 ... (remaining 11224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1898 0.088 - 0.177: 793 0.177 - 0.265: 89 0.265 - 0.354: 16 0.354 - 0.442: 13 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C3' ADP D 402 " pdb=" C2' ADP D 402 " pdb=" C4' ADP D 402 " pdb=" O3' ADP D 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.95 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C3' ADP C 402 " pdb=" C2' ADP C 402 " pdb=" C4' ADP C 402 " pdb=" O3' ADP C 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.95 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' ADP A 402 " pdb=" C2' ADP A 402 " pdb=" C4' ADP A 402 " pdb=" O3' ADP A 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.95 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 2806 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " -0.145 2.00e-02 2.50e+03 6.78e-02 1.15e+02 pdb=" CG TRP C 340 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.145 2.00e-02 2.50e+03 6.78e-02 1.15e+02 pdb=" CG TRP B 340 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.145 2.00e-02 2.50e+03 6.78e-02 1.15e+02 pdb=" CG TRP A 340 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.056 2.00e-02 2.50e+03 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 15 2.45 - 3.06: 9577 3.06 - 3.67: 25864 3.67 - 4.29: 40802 4.29 - 4.90: 66843 Nonbonded interactions: 143101 Sorted by model distance: nonbonded pdb=" OG SER B 14 " pdb=" O3B ADP B 402 " model vdw 1.834 2.440 nonbonded pdb=" OG SER A 14 " pdb=" O3B ADP A 402 " model vdw 1.834 2.440 nonbonded pdb=" OG SER E 14 " pdb=" O3B ADP E 402 " model vdw 1.834 2.440 nonbonded pdb=" OG SER D 14 " pdb=" O3B ADP D 402 " model vdw 1.835 2.440 nonbonded pdb=" OG SER C 14 " pdb=" O3B ADP C 402 " model vdw 1.835 2.440 ... (remaining 143096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.530 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 49.140 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.119 18515 Z= 0.935 Angle : 1.858 15.348 25073 Z= 1.234 Chirality : 0.092 0.442 2809 Planarity : 0.024 0.228 3184 Dihedral : 12.632 113.798 6947 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.53 % Favored : 97.25 % Rotamer: Outliers : 0.25 % Allowed : 1.32 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.15), residues: 2256 helix: -3.97 (0.09), residues: 832 sheet: -1.82 (0.22), residues: 435 loop : -0.46 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.145 0.025 TRP B 340 HIS 0.004 0.001 HIS B 101 PHE 0.059 0.009 PHE I 71 TYR 0.093 0.015 TYR I 117 ARG 0.017 0.003 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 566 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 71 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 82 MET cc_start: 0.9465 (tpt) cc_final: 0.8628 (tpt) REVERT: B 136 ILE cc_start: 0.9432 (mm) cc_final: 0.9229 (mm) REVERT: C 82 MET cc_start: 0.9501 (tpt) cc_final: 0.8832 (tpt) REVERT: C 111 ASN cc_start: 0.8908 (t0) cc_final: 0.8628 (t0) REVERT: D 111 ASN cc_start: 0.8939 (t0) cc_final: 0.8359 (t0) REVERT: E 78 ASN cc_start: 0.8045 (t0) cc_final: 0.7832 (t0) REVERT: E 111 ASN cc_start: 0.8712 (t0) cc_final: 0.7832 (t0) REVERT: E 159 VAL cc_start: 0.9130 (p) cc_final: 0.8896 (m) REVERT: H 81 ARG cc_start: 0.8856 (mmt-90) cc_final: 0.8538 (mmt-90) REVERT: H 143 ILE cc_start: 0.9065 (tt) cc_final: 0.8852 (tt) REVERT: I 54 GLN cc_start: 0.7630 (pt0) cc_final: 0.7385 (pt0) REVERT: I 81 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.7831 (mmt-90) REVERT: J 81 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8150 (mpt180) REVERT: J 143 ILE cc_start: 0.9011 (tt) cc_final: 0.8746 (tt) outliers start: 5 outliers final: 0 residues processed: 566 average time/residue: 0.2939 time to fit residues: 252.4009 Evaluate side-chains 336 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 115 ASN A 162 ASN A 353 GLN B 12 ASN B 87 HIS B 115 ASN B 162 ASN B 353 GLN B 360 GLN C 12 ASN C 87 HIS C 162 ASN C 371 HIS D 12 ASN D 87 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 353 GLN E 12 ASN E 87 HIS E 162 ASN E 353 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18515 Z= 0.152 Angle : 0.589 9.327 25073 Z= 0.294 Chirality : 0.045 0.157 2809 Planarity : 0.004 0.036 3184 Dihedral : 6.177 67.515 2536 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.24 % Allowed : 8.03 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2256 helix: -3.00 (0.12), residues: 872 sheet: -1.08 (0.24), residues: 461 loop : 0.22 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 340 HIS 0.002 0.001 HIS B 173 PHE 0.010 0.001 PHE I 38 TYR 0.009 0.001 TYR J 82 ARG 0.006 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 340 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9438 (mm) cc_final: 0.9077 (mm) REVERT: A 296 ASN cc_start: 0.8657 (m-40) cc_final: 0.8454 (m-40) REVERT: B 136 ILE cc_start: 0.9476 (mm) cc_final: 0.9179 (mt) REVERT: B 176 MET cc_start: 0.7965 (mmm) cc_final: 0.7757 (mmp) REVERT: D 344 SER cc_start: 0.8673 (t) cc_final: 0.8401 (t) REVERT: E 136 ILE cc_start: 0.9177 (mm) cc_final: 0.8848 (mt) REVERT: H 3 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7807 (m) REVERT: H 143 ILE cc_start: 0.8941 (tt) cc_final: 0.8668 (tt) REVERT: I 162 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6582 (mp0) REVERT: J 143 ILE cc_start: 0.8931 (tt) cc_final: 0.8602 (tt) outliers start: 44 outliers final: 26 residues processed: 365 average time/residue: 0.2565 time to fit residues: 149.1965 Evaluate side-chains 306 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain J residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 275 HIS A 353 GLN B 360 GLN C 275 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS E 59 GLN H 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18515 Z= 0.368 Angle : 0.672 8.076 25073 Z= 0.334 Chirality : 0.049 0.166 2809 Planarity : 0.004 0.038 3184 Dihedral : 5.954 46.620 2534 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.30 % Allowed : 10.47 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2256 helix: -2.66 (0.14), residues: 899 sheet: -0.92 (0.24), residues: 486 loop : 0.13 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 340 HIS 0.004 0.001 HIS A 101 PHE 0.013 0.002 PHE J 38 TYR 0.013 0.002 TYR A 218 ARG 0.011 0.001 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 357 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9598 (mm) cc_final: 0.9300 (mm) REVERT: A 283 MET cc_start: 0.8923 (mmm) cc_final: 0.8575 (mmm) REVERT: B 24 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: B 136 ILE cc_start: 0.9621 (mm) cc_final: 0.9340 (mt) REVERT: B 313 MET cc_start: 0.8588 (tpp) cc_final: 0.8333 (mmm) REVERT: C 136 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9255 (mm) REVERT: C 206 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7382 (tpp80) REVERT: C 334 GLU cc_start: 0.8312 (pm20) cc_final: 0.8001 (pp20) REVERT: E 68 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7807 (mttp) REVERT: H 31 LYS cc_start: 0.8421 (mptt) cc_final: 0.7845 (mttm) REVERT: H 143 ILE cc_start: 0.9092 (tt) cc_final: 0.8775 (tt) REVERT: I 79 ASP cc_start: 0.8445 (t0) cc_final: 0.7768 (m-30) REVERT: J 27 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7387 (pt0) REVERT: J 81 ARG cc_start: 0.8759 (mmt90) cc_final: 0.8486 (mmt180) REVERT: J 143 ILE cc_start: 0.9034 (tt) cc_final: 0.8814 (tt) outliers start: 65 outliers final: 43 residues processed: 391 average time/residue: 0.2698 time to fit residues: 165.8590 Evaluate side-chains 335 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 289 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 145 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 101 HIS B 275 HIS C 275 HIS D 101 HIS D 115 ASN D 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18515 Z= 0.297 Angle : 0.613 8.655 25073 Z= 0.301 Chirality : 0.047 0.196 2809 Planarity : 0.004 0.036 3184 Dihedral : 5.556 35.177 2534 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.66 % Allowed : 12.75 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 2256 helix: -2.43 (0.14), residues: 914 sheet: -0.31 (0.26), residues: 416 loop : 0.01 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS H 133 PHE 0.009 0.001 PHE H 103 TYR 0.019 0.001 TYR D 279 ARG 0.005 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 311 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7506 (ptm) cc_final: 0.7270 (ttp) REVERT: A 136 ILE cc_start: 0.9588 (mm) cc_final: 0.9300 (mm) REVERT: A 283 MET cc_start: 0.8850 (mmm) cc_final: 0.8392 (mmm) REVERT: A 299 MET cc_start: 0.8393 (mtm) cc_final: 0.8111 (mtm) REVERT: B 24 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: B 132 MET cc_start: 0.7641 (tmm) cc_final: 0.7284 (tmm) REVERT: B 136 ILE cc_start: 0.9623 (mm) cc_final: 0.9329 (mt) REVERT: B 249 THR cc_start: 0.8486 (t) cc_final: 0.8262 (p) REVERT: B 313 MET cc_start: 0.8518 (tpp) cc_final: 0.8232 (mmm) REVERT: C 206 ARG cc_start: 0.7687 (ttt-90) cc_final: 0.7351 (tpp80) REVERT: C 334 GLU cc_start: 0.8324 (pm20) cc_final: 0.7992 (pp20) REVERT: D 205 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: E 68 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7893 (mttp) REVERT: H 31 LYS cc_start: 0.8216 (mptt) cc_final: 0.7772 (mttm) REVERT: H 143 ILE cc_start: 0.9119 (tt) cc_final: 0.8764 (tt) REVERT: J 27 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: J 81 ARG cc_start: 0.8757 (mmt90) cc_final: 0.8495 (mmt-90) REVERT: J 143 ILE cc_start: 0.9077 (tt) cc_final: 0.8843 (tt) outliers start: 72 outliers final: 49 residues processed: 355 average time/residue: 0.2854 time to fit residues: 157.4646 Evaluate side-chains 332 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 280 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 145 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN C 101 HIS E 101 HIS I 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 18515 Z= 0.375 Angle : 0.655 9.572 25073 Z= 0.323 Chirality : 0.049 0.208 2809 Planarity : 0.004 0.038 3184 Dihedral : 5.739 37.676 2534 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.40 % Allowed : 14.08 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2256 helix: -2.34 (0.15), residues: 909 sheet: -0.41 (0.26), residues: 416 loop : -0.16 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS B 173 PHE 0.011 0.001 PHE J 101 TYR 0.015 0.002 TYR D 279 ARG 0.006 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 289 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9617 (mm) cc_final: 0.9335 (mm) REVERT: A 283 MET cc_start: 0.8946 (mmm) cc_final: 0.8423 (mmm) REVERT: B 24 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 132 MET cc_start: 0.7607 (tmm) cc_final: 0.7333 (tmm) REVERT: B 292 ASP cc_start: 0.8444 (t0) cc_final: 0.8215 (t0) REVERT: B 313 MET cc_start: 0.8579 (tpp) cc_final: 0.8287 (mmm) REVERT: C 123 MET cc_start: 0.8242 (tpp) cc_final: 0.7984 (tpp) REVERT: C 334 GLU cc_start: 0.8283 (pm20) cc_final: 0.7980 (pp20) REVERT: E 176 MET cc_start: 0.7639 (mmp) cc_final: 0.7422 (mmp) REVERT: H 31 LYS cc_start: 0.8294 (mptt) cc_final: 0.7825 (mttm) REVERT: H 143 ILE cc_start: 0.9163 (tt) cc_final: 0.8762 (tt) REVERT: J 31 LYS cc_start: 0.8442 (mptt) cc_final: 0.7970 (mttm) REVERT: J 81 ARG cc_start: 0.8816 (mmt90) cc_final: 0.8574 (mmt-90) REVERT: J 143 ILE cc_start: 0.9091 (tt) cc_final: 0.8869 (tt) outliers start: 67 outliers final: 49 residues processed: 331 average time/residue: 0.2711 time to fit residues: 141.0470 Evaluate side-chains 315 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 265 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 145 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18515 Z= 0.344 Angle : 0.632 10.364 25073 Z= 0.310 Chirality : 0.048 0.218 2809 Planarity : 0.004 0.037 3184 Dihedral : 5.654 36.795 2534 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.46 % Allowed : 14.84 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2256 helix: -2.16 (0.16), residues: 891 sheet: -0.45 (0.26), residues: 416 loop : -0.21 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS B 173 PHE 0.009 0.001 PHE J 101 TYR 0.013 0.001 TYR B 218 ARG 0.008 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 277 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9609 (mm) cc_final: 0.9328 (mm) REVERT: A 283 MET cc_start: 0.8898 (mmm) cc_final: 0.8482 (mmm) REVERT: B 132 MET cc_start: 0.7533 (tmm) cc_final: 0.7329 (tmm) REVERT: B 313 MET cc_start: 0.8546 (tpp) cc_final: 0.8281 (mmm) REVERT: C 99 GLU cc_start: 0.7011 (pm20) cc_final: 0.6726 (pm20) REVERT: C 334 GLU cc_start: 0.8231 (pm20) cc_final: 0.7978 (pp20) REVERT: E 68 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7806 (mttp) REVERT: H 31 LYS cc_start: 0.8277 (mptt) cc_final: 0.7781 (mttm) REVERT: H 143 ILE cc_start: 0.9141 (tt) cc_final: 0.8760 (tt) REVERT: J 27 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: J 31 LYS cc_start: 0.8479 (mptt) cc_final: 0.8092 (mttm) REVERT: J 81 ARG cc_start: 0.8805 (mmt90) cc_final: 0.8527 (mmt-90) REVERT: J 143 ILE cc_start: 0.9110 (tt) cc_final: 0.8876 (tt) outliers start: 68 outliers final: 55 residues processed: 321 average time/residue: 0.2567 time to fit residues: 130.5875 Evaluate side-chains 328 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 145 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18515 Z= 0.196 Angle : 0.555 7.905 25073 Z= 0.269 Chirality : 0.044 0.155 2809 Planarity : 0.003 0.034 3184 Dihedral : 5.092 34.091 2534 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.59 % Allowed : 16.36 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2256 helix: -1.93 (0.16), residues: 891 sheet: -0.38 (0.26), residues: 416 loop : -0.06 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 356 HIS 0.003 0.001 HIS C 87 PHE 0.008 0.001 PHE D 352 TYR 0.010 0.001 TYR D 279 ARG 0.006 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7420 (ptm) cc_final: 0.7201 (ttp) REVERT: A 136 ILE cc_start: 0.9598 (mm) cc_final: 0.9312 (mm) REVERT: A 283 MET cc_start: 0.8864 (mmm) cc_final: 0.8488 (mmm) REVERT: A 299 MET cc_start: 0.8430 (mtm) cc_final: 0.8117 (mtm) REVERT: B 132 MET cc_start: 0.7514 (tmm) cc_final: 0.7303 (tmm) REVERT: B 292 ASP cc_start: 0.8560 (t0) cc_final: 0.8173 (t0) REVERT: B 313 MET cc_start: 0.8493 (tpp) cc_final: 0.8253 (mmm) REVERT: C 334 GLU cc_start: 0.8178 (pm20) cc_final: 0.7919 (pp20) REVERT: E 68 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7775 (mttp) REVERT: E 299 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7839 (mtp) REVERT: H 31 LYS cc_start: 0.8256 (mptt) cc_final: 0.7766 (mttm) REVERT: H 143 ILE cc_start: 0.9162 (tt) cc_final: 0.8760 (tt) REVERT: J 31 LYS cc_start: 0.8419 (mptt) cc_final: 0.8017 (mttm) REVERT: J 81 ARG cc_start: 0.8724 (mmt90) cc_final: 0.8490 (mmt-90) REVERT: J 143 ILE cc_start: 0.9028 (tt) cc_final: 0.8780 (tt) outliers start: 51 outliers final: 39 residues processed: 317 average time/residue: 0.2701 time to fit residues: 135.4309 Evaluate side-chains 309 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18515 Z= 0.269 Angle : 0.591 9.457 25073 Z= 0.288 Chirality : 0.046 0.169 2809 Planarity : 0.004 0.035 3184 Dihedral : 5.177 34.462 2534 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.54 % Allowed : 16.67 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2256 helix: -1.89 (0.16), residues: 891 sheet: -0.38 (0.26), residues: 416 loop : -0.11 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.002 0.001 HIS B 173 PHE 0.009 0.001 PHE J 101 TYR 0.011 0.001 TYR D 279 ARG 0.004 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 281 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7472 (ptm) cc_final: 0.7246 (ttp) REVERT: A 136 ILE cc_start: 0.9622 (mm) cc_final: 0.9346 (mm) REVERT: A 283 MET cc_start: 0.8884 (mmm) cc_final: 0.8492 (mmm) REVERT: A 299 MET cc_start: 0.8476 (mtm) cc_final: 0.8189 (mtm) REVERT: B 136 ILE cc_start: 0.9609 (mm) cc_final: 0.9386 (mt) REVERT: B 206 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.7704 (ttt90) REVERT: B 292 ASP cc_start: 0.8593 (t0) cc_final: 0.8006 (t0) REVERT: B 313 MET cc_start: 0.8543 (tpp) cc_final: 0.8298 (mmm) REVERT: C 99 GLU cc_start: 0.6852 (pm20) cc_final: 0.6614 (pm20) REVERT: C 334 GLU cc_start: 0.8162 (pm20) cc_final: 0.7944 (pp20) REVERT: E 68 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7731 (mttp) REVERT: H 31 LYS cc_start: 0.8203 (mptt) cc_final: 0.7752 (mttm) REVERT: H 143 ILE cc_start: 0.9168 (tt) cc_final: 0.8774 (tt) REVERT: J 31 LYS cc_start: 0.8401 (mptt) cc_final: 0.8020 (mttm) REVERT: J 79 ASP cc_start: 0.8183 (t0) cc_final: 0.7880 (m-30) REVERT: J 81 ARG cc_start: 0.8792 (mmt90) cc_final: 0.8578 (mmt-90) REVERT: J 143 ILE cc_start: 0.9069 (tt) cc_final: 0.8822 (tt) outliers start: 50 outliers final: 46 residues processed: 312 average time/residue: 0.2744 time to fit residues: 134.3167 Evaluate side-chains 316 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 270 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 145 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18515 Z= 0.218 Angle : 0.573 10.778 25073 Z= 0.275 Chirality : 0.045 0.174 2809 Planarity : 0.003 0.034 3184 Dihedral : 4.967 33.266 2534 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.59 % Allowed : 16.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2256 helix: -1.66 (0.17), residues: 861 sheet: -0.36 (0.26), residues: 416 loop : 0.15 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS C 87 PHE 0.008 0.001 PHE I 101 TYR 0.010 0.001 TYR D 279 ARG 0.003 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7441 (ptm) cc_final: 0.7218 (ttp) REVERT: A 136 ILE cc_start: 0.9610 (mm) cc_final: 0.9332 (mm) REVERT: A 283 MET cc_start: 0.8833 (mmm) cc_final: 0.8464 (mmm) REVERT: A 299 MET cc_start: 0.8435 (mtm) cc_final: 0.8119 (mtm) REVERT: B 136 ILE cc_start: 0.9604 (mm) cc_final: 0.9372 (mt) REVERT: B 292 ASP cc_start: 0.8568 (t0) cc_final: 0.8014 (t0) REVERT: B 313 MET cc_start: 0.8512 (tpp) cc_final: 0.8268 (mmm) REVERT: C 99 GLU cc_start: 0.6799 (pm20) cc_final: 0.6579 (pm20) REVERT: C 334 GLU cc_start: 0.8129 (pm20) cc_final: 0.7925 (pp20) REVERT: E 68 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7776 (mttp) REVERT: E 136 ILE cc_start: 0.9541 (mm) cc_final: 0.9164 (mm) REVERT: H 31 LYS cc_start: 0.8221 (mptt) cc_final: 0.7745 (mttm) REVERT: H 143 ILE cc_start: 0.9169 (tt) cc_final: 0.8762 (tt) REVERT: J 31 LYS cc_start: 0.8413 (mptt) cc_final: 0.8051 (mttm) REVERT: J 81 ARG cc_start: 0.8720 (mmt90) cc_final: 0.8492 (mmt-90) REVERT: J 143 ILE cc_start: 0.9023 (tt) cc_final: 0.8755 (tt) outliers start: 51 outliers final: 46 residues processed: 312 average time/residue: 0.2650 time to fit residues: 130.9194 Evaluate side-chains 315 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 269 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 150 optimal weight: 0.2980 chunk 227 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18515 Z= 0.251 Angle : 0.592 11.844 25073 Z= 0.285 Chirality : 0.046 0.170 2809 Planarity : 0.004 0.034 3184 Dihedral : 5.014 33.372 2534 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.54 % Allowed : 16.92 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2256 helix: -1.61 (0.17), residues: 856 sheet: -0.36 (0.26), residues: 416 loop : 0.11 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.002 0.001 HIS C 87 PHE 0.008 0.001 PHE J 101 TYR 0.011 0.001 TYR I 117 ARG 0.004 0.000 ARG C 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 277 time to evaluate : 2.195 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7484 (ptm) cc_final: 0.7267 (ttp) REVERT: A 136 ILE cc_start: 0.9619 (mm) cc_final: 0.9344 (mm) REVERT: A 283 MET cc_start: 0.8849 (mmm) cc_final: 0.8481 (mmm) REVERT: A 299 MET cc_start: 0.8461 (mtm) cc_final: 0.8144 (mtm) REVERT: B 136 ILE cc_start: 0.9603 (mm) cc_final: 0.9378 (mt) REVERT: B 292 ASP cc_start: 0.8598 (t0) cc_final: 0.8042 (t0) REVERT: B 313 MET cc_start: 0.8527 (tpp) cc_final: 0.8277 (mmm) REVERT: C 334 GLU cc_start: 0.8155 (pm20) cc_final: 0.7932 (pp20) REVERT: E 68 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7731 (mttp) REVERT: H 31 LYS cc_start: 0.8218 (mptt) cc_final: 0.7756 (mttm) REVERT: H 143 ILE cc_start: 0.9154 (tt) cc_final: 0.8781 (tt) REVERT: J 31 LYS cc_start: 0.8403 (mptt) cc_final: 0.7997 (mttm) REVERT: J 79 ASP cc_start: 0.8192 (t0) cc_final: 0.7905 (m-30) REVERT: J 86 ASP cc_start: 0.8268 (t0) cc_final: 0.8043 (t0) REVERT: J 143 ILE cc_start: 0.9007 (tt) cc_final: 0.8732 (tt) outliers start: 50 outliers final: 48 residues processed: 307 average time/residue: 0.2713 time to fit residues: 131.3806 Evaluate side-chains 321 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 273 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 145 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.0020 chunk 159 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.105145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.093280 restraints weight = 24314.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.095040 restraints weight = 16502.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.096349 restraints weight = 12365.431| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18515 Z= 0.151 Angle : 0.547 11.740 25073 Z= 0.260 Chirality : 0.043 0.186 2809 Planarity : 0.003 0.034 3184 Dihedral : 4.562 30.240 2534 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.58 % Allowed : 18.09 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2256 helix: -1.36 (0.18), residues: 836 sheet: -0.09 (0.27), residues: 392 loop : 0.31 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.003 0.000 HIS C 87 PHE 0.007 0.001 PHE D 352 TYR 0.010 0.001 TYR D 279 ARG 0.003 0.000 ARG C 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3578.18 seconds wall clock time: 66 minutes 12.53 seconds (3972.53 seconds total)